BN1554 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 3 8.3920e-07 5.9170e-04
Layer 4 8.5203e-06 1.2047e-03
Layer 2 5.5959e-05 3.4875e-03
Layer 5 8.3219e-04 4.3920e-03
Layer 6 1.8256e-03 5.9423e-03
Layer 1 4.1174e-01 4.1540e-01
WM 8.8505e-01 3.3970e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
C9orf16 Expression Distribution
Gene Specificity Score (GSS)
C9orf16 GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
C9orf16 Layer 3 3.1797 0.7696
ATP5F1A Layer 3 2.6074 0.7677
SH3GL2 Layer 3 2.4727 0.7660
ATP5MPL Layer 3 2.5273 0.7549
ATP5IF1 Layer 3 2.5391 0.7549
SPTAN1 Layer 3 2.5391 0.7524
MDH1 Layer 4 2.6836 0.7516
ATP5MC3 Layer 3 2.7305 0.7507
BEX1 Layer 3 2.4121 0.7498
CABP1 Layer 3 2.7656 0.7494
FXYD7 Layer 4 2.8281 0.7488
COX7A1 Layer 3 2.5176 0.7481
UQCRH Layer 3 2.5840 0.7478
RAB3A Layer 4 2.7012 0.7476
CHCHD10 Layer 3 2.7793 0.7471
PINK1 Layer 3 2.5059 0.7468
CLTC Layer 4 2.6191 0.7467
CLSTN1 Layer 4 2.7246 0.7461
ATP2B2 Layer 4 3.2012 0.7456
MGST3 Layer 3 2.5508 0.7453
NDUFB1 Layer 4 2.6543 0.7450
SNCB Layer 4 2.9082 0.7445
OAZ1 Layer 3 2.3965 0.7442
SLC1A2 Layer 3 2.5840 0.7411
HSPH1 Layer 4 2.9219 0.7406
COX7B Layer 4 2.7480 0.7396
SCG5 Layer 4 2.7246 0.7387
MORF4L1 Layer 4 2.4570 0.7375
EEF1A2 Layer 3 2.8770 0.7370
ALDOC Layer 3 2.5898 0.7367
INA Layer 3 2.8594 0.7366
PGK1 Layer 3 2.6484 0.7364
LDHB Layer 4 2.6426 0.7362
NDUFB2 Layer 3 2.5566 0.7360
KHDRBS3 Layer 4 2.8027 0.7358
ATP5PF Layer 3 2.5176 0.7358
BASP1 Layer 4 2.6426 0.7357
PRDX2 Layer 4 2.5898 0.7355
PKM Layer 4 2.6367 0.7354
NPTN Layer 4 2.6250 0.7351
GNG3 Layer 3 2.6133 0.7350
GPI Layer 4 2.5117 0.7348
ATP5MC1 Layer 4 2.6309 0.7336
UQCR10 Layer 4 2.4668 0.7334
PPP3CA Layer 2 2.5664 0.7333
MEF2C Layer 3 2.8711 0.7330
GHITM Layer 4 2.5391 0.7326
ATP5PD Layer 4 2.4727 0.7325
UQCRB Layer 3 2.3438 0.7322
ATP1A1 Layer 3 2.6777 0.7322

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1554
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1554_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1554/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1554/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1554/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1554/report/PD/BN1554_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1554/report/PD/BN1554_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 05:04:49
  • Number of Processes: 10
  • Spending Time: 0h 4m